Merge remote-tracking branch 'origin/main' into overview-change-loader

.dockerignore

@@ -2,5 +2,4 @@
 build
 dist
 node_modules
-server.env
 www

.eslintrc.js

@@ -19,6 +19,7 @@ module.exports = {
     'plugin:@typescript-eslint/recommended',
     'plugin:prettier/recommended',
     'plugin:react-hooks/recommended',
+    'plugin:react/jsx-runtime',
   ],
   rules: {
     'react/prop-types': 'off', // disable prop-types since we're using TypeScript
@@ -38,6 +39,7 @@ module.exports = {
       },
     ],
     semi: ['error', 'always'],
+    'react/react-in-jsx-scope': 'off',
   },
   settings: {
     react: {

.github/workflows/build.yml

@@ -25,7 +25,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Run Bento build action
-        uses: bento-platform/bento_build_action@v0.11.1
+        uses: bento-platform/bento_build_action@v1.0.0
         with:
           registry: ghcr.io
           registry-username: ${{ github.actor }}

.gitignore

@@ -1,11 +1,7 @@
-client.env
-server.env
-
 build/*
 node_modules/*
 dist/*
 .DS_Store
-.prettierrc
 .idea/
 .vscode/
 www/

Dockerfile

@@ -1,51 +1,60 @@
-FROM --platform=$BUILDPLATFORM node:20-bookworm-slim as nodebuilder
+FROM --platform=$BUILDPLATFORM node:20-bookworm-slim AS build
 
-WORKDIR /node
+# Build bento_public with NodeJS + Webpack
+#  - Use BUILDPLATFORM for running webpack, since it should perform a lot better.
+#  - Then, the resulting built files will be copied to a TARGETPLATFORM-based final image.
+
+WORKDIR /bento-public
 
-# Install using just package-lock.json with npm ci
 COPY package.json .
 COPY package-lock.json .
+
 RUN npm ci
 
-# Build the web application
-COPY tsconfig.json .
+# Explicitly choose what to copy to speed up builds
+#  - Copy in build requirements
+COPY create_service_info.js .
 COPY webpack.config.js .
+COPY tsconfig.json .
+#  - Copy in source code
 COPY src src
-RUN mkdir -p build/www
-RUN npm run build
-
-
-FROM golang:1.21-bookworm as gobuilder
 
-RUN apt-get update -y && \
-    apt-get upgrade -y && \
-    apt-get install -y git
-
-WORKDIR /build
-
-# Only copy the files that are needed!
-COPY go.mod .
-COPY go.sum .
-COPY main.go .
+RUN npm run build
 
-RUN go build -o ./reactapp
+FROM nginx:1.26
 
+# Install node so that we can run the create_config_prod.js & create_service_info.js scripts
+RUN curl -fsSL https://deb.nodesource.com/setup_20.x | bash - && \
+    apt-get update -y && \
+    apt-get install -y ca-certificates curl gnupg && \
+    mkdir -p /etc/apt/keyrings && \
+    curl -fsSL https://deb.nodesource.com/gpgkey/nodesource-repo.gpg.key | \
+      gpg --dearmor -o /etc/apt/keyrings/nodesource.gpg && \
+    echo "deb [signed-by=/etc/apt/keyrings/nodesource.gpg] https://deb.nodesource.com/node_20.x nodistro main" | \
+      tee /etc/apt/sources.list.d/nodesource.list && \
+    apt-get install -y nodejs && \
+    rm -rf /var/lib/apt/lists/*
 
-FROM ghcr.io/bento-platform/bento_base_image:node-debian-2024.07.09
+# Serve bento_public with NGINX; copy in configuration
+COPY nginx.conf /etc/nginx/nginx.conf
 
-ENV BENTO_PUBLIC_PACKAGE_JSON_PATH=/bento-public/package.json
 WORKDIR /bento-public
 
-COPY entrypoint.bash .
-COPY package.json .
+# In general, we want to copy files in order of least -> most changed for layer caching reasons.
+
+# - Copy in LICENSE so that people can see it if they explore the image contents
+COPY LICENSE .
+# - Copy in the production config generation script
 COPY create_config_prod.js .
+# - Copy in the service info generator
+COPY create_service_info.js .
+# - Copy in the entrypoint, which writes the config file and starts NGINX
 COPY run.bash .
+# - Copy in package.json to provide version to scripts
+COPY package.json .
+# - Copy webpack-built source code from the build stage to the final image
+#    - copy this last, since it changes more often than everything above it
+#    - this way we can cache layers
+COPY --from=build /bento-public/dist ./dist
 
-# Copy web app
-COPY --from=nodebuilder /node/build/www /bento-public/www
-
-# Copy server
-COPY --from=gobuilder /build/reactapp /bento-public/reactapp
-
-ENTRYPOINT [ "/bin/bash", "./entrypoint.bash" ]
-CMD [ "/bin/bash", "./run.bash" ]
+CMD ["bash", "./run.bash"]

README.md

@@ -3,32 +3,10 @@
 A publicly accessible portal for clinical datasets, where users are able to see high-level statistics of the data 
 available through predefined variables of interest and search the data using limited variables at a time. This portal 
 allows users to gain a generic understanding of the data available (secure and firewalled) without the need to access 
-it directly. Initially, this portal facilitates the search in English language only, but the French language will be 
-added at a later time.
+it directly.
 
 ## Prerequisites:
 - Node Package Manager
-- Go version >= 1.19
-
-## Getting started:
-
-First, run
-```bash
-cp etc/example.server.env server.env
-```
-and modify the contents according to your needs.
-
-If needed, install the relevant Go dependencies:
-
-```bash
-go mod download
-```
-
-Finally, install the NPM dependencies and run the build process:
-```bash
-npm install
-npm run gobuild
-```
 
 ## Translations in dev mode
 Add your English to French translations in `www/public/locales/fr/translation_fr.json` for them to appear on the website.

create_config_prod.js

@@ -1,4 +1,4 @@
-const parseBoolean = (value) => ['true', '1', 'yes'].includes((value || '').toLocaleLowerCase());
+const parseBoolean = (value) => ['true', 't', '1', 'yes'].includes((value || '').toLocaleLowerCase());
 
 const siteConfig = {
   CLIENT_NAME: process.env.BENTO_PUBLIC_CLIENT_NAME || null,

create_service_info.js

@@ -0,0 +1,59 @@
+/* eslint-disable @typescript-eslint/no-var-requires */
+const childProcess = require('child_process');
+const packageData = require('./package.json');
+
+const nodeEnv = process.env.NODE_ENV || 'production';
+
+const serviceType = {
+  group: 'ca.c3g.bento',
+  artifact: 'public',
+  version: packageData.version,
+};
+
+const serviceID = process.env.SERVICE_ID || `${serviceType.group}:${serviceType.artifact}`;
+
+const serviceInfo = {
+  id: serviceID,
+  name: 'Bento Public',
+  description: 'Public web interface for the Bento platform.',
+  type: serviceType,
+  version: packageData.version,
+  environment: nodeEnv === 'production' ? 'prod' : 'dev',
+  organization: {
+    name: 'C3G',
+    url: 'https://www.computationalgenomics.ca',
+  },
+  contactUrl: 'mailto:[email protected]',
+  bento: {
+    serviceKind: 'public',
+  },
+};
+
+const hasGit = (() => {
+  try {
+    return childProcess.execSync('which git').toString().trim() === '';
+  } catch (_e) {
+    // Exit code 1 (git not found)
+    return false;
+  }
+})();
+const git = (cmd) => childProcess.execSync(`git ${cmd}`).toString().trim();
+if (nodeEnv === 'development' && hasGit) {
+  try {
+    serviceInfo.bento.gitTag = git('describe --tags --abbrev=0');
+    serviceInfo.bento.gitBranch = git('branch --show-current');
+    serviceInfo.bento.gitCommit = git('rev-parse HEAD');
+  } catch (e) {
+    console.warn(`Could not get git information (${e})`);
+  }
+} else if (!hasGit) {
+  console.warn('Could not get git information (missing git)');
+}
+
+if (typeof require !== 'undefined' && require.main === module) {
+  console.log(JSON.stringify(serviceInfo, null, 2));
+}
+
+module.exports = {
+  serviceInfo,
+};

dev.Dockerfile

@@ -1,30 +1,22 @@
-FROM ghcr.io/bento-platform/bento_base_image:node-debian-2024.07.09
-
-RUN apt-get update -y && \
-    apt-get install -y ca-certificates
-
-# Use bookworm-backports to get go 1.21 instead of 1.19
-# Install lsof to help killing the PID binding the port if needed
-RUN echo "deb https://deb.debian.org/debian bookworm-backports main contrib non-free" >> /etc/apt/sources.list && \
-    echo "deb-src https://deb.debian.org/debian bookworm-backports main contrib non-free" >> /etc/apt/sources.list && \
-    apt-get update -y && \
-    apt-get upgrade -y && \
-    apt-get -t bookworm-backports install -y golang-go lsof && \
-    rm -rf /var/lib/apt/lists/*
+FROM --platform=$BUILDPLATFORM node:20-bookworm-slim AS install
 
 WORKDIR /bento-public
 
 COPY package.json .
 COPY package-lock.json .
 
-# Install NPM dev/prod dependencies to get Nodemon - we will need to fix the permissions of node_modules after
 RUN npm ci
 
-# Don't copy code in, since we expect it to be mounted via volume
+FROM ghcr.io/bento-platform/bento_base_image:node-debian-2024.10.01
+
+LABEL org.opencontainers.image.description="Local development image for Bento Public."
+
+WORKDIR /bento-public
 
-COPY entrypoint.bash .
 COPY run.dev.bash .
-COPY nodemon.json .
+COPY package.json .
+COPY package-lock.json .
+
+COPY --from=install /bento-public/node_modules ./node_modules
 
-ENTRYPOINT [ "bash", "./entrypoint.bash" ]
 CMD [ "bash", "./run.dev.bash" ]